I have just released updated v1.4.4 of phpwcms (r381) which adds support for custom JavaScript library in the frontend. By default jQuery 1.3, MooTools 1.1 and MooTools 1.2 are supported. But if you like it should be no problem to enhance it by your own custom lib.

Please be aware when updating your current installation - older JS related things might no longer work. So always keep a backup and be very careful.